data_5K7D # _entry.id 5K7D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 5K7D pdb_00005k7d 10.2210/pdb5k7d/pdb WWPDB D_1000221853 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2016-07-13 2 'Structure model' 1 1 2016-07-27 3 'Structure model' 1 2 2016-08-31 4 'Structure model' 1 3 2024-03-06 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' pdbx_struct_oper_list 6 4 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.value' 6 4 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 7 4 'Structure model' '_struct_conn.pdbx_dist_value' 8 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5K7D _pdbx_database_status.recvd_initial_deposition_date 2016-05-26 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 5K7C PDB . unspecified 5K7E PDB . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ren, A.' 1 'Patel, D.' 2 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Nat.Chem.Biol. _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1552-4469 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 12 _citation.language ? _citation.page_first 702 _citation.page_last 708 _citation.title 'Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage.' _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/nchembio.2125 _citation.pdbx_database_id_PubMed 27398999 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ren, A.' 1 ? primary 'Vusurovic, N.' 2 ? primary 'Gebetsberger, J.' 3 ? primary 'Gao, P.' 4 ? primary 'Juen, M.' 5 ? primary 'Kreutz, C.' 6 ? primary 'Micura, R.' 7 ? primary 'Patel, D.J.' 8 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'RNA 47-MER' 15096.936 1 ? ? ? ? 2 polymer syn 'DNA/RNA 11-MER' 3514.178 1 ? ? ? ? 3 non-polymer syn 'IRIDIUM HEXAMMINE ION' 294.400 2 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 5 ? ? ? ? 5 water nat water 18.015 15 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polydeoxyribonucleotide/polyribonucleotide hybrid' no no CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAU CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAU A ? 2 'polydeoxyribonucleotide/polyribonucleotide hybrid' no no 'AUCAG(DG)UGCAA' AUCAGGUGCAA B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'IRIDIUM HEXAMMINE ION' IRI 4 'MAGNESIUM ION' MG 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 U n 1 4 G n 1 5 G n 1 6 U n 1 7 U n 1 8 A n 1 9 G n 1 10 G n 1 11 G n 1 12 C n 1 13 C n 1 14 A n 1 15 C n 1 16 G n 1 17 U n 1 18 U n 1 19 A n 1 20 A n 1 21 A n 1 22 U n 1 23 A n 1 24 G n 1 25 U n 1 26 U n 1 27 G n 1 28 C n 1 29 U n 1 30 U n 1 31 A n 1 32 A n 1 33 G n 1 34 C n 1 35 C n 1 36 C n 1 37 U n 1 38 A n 1 39 A n 1 40 G n 1 41 C n 1 42 G n 1 43 U n 1 44 U n 1 45 G n 1 46 A n 1 47 U n 2 1 A n 2 2 U n 2 3 C n 2 4 A n 2 5 G n 2 6 DG n 2 7 U n 2 8 G n 2 9 C n 2 10 A n 2 11 A n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 47 'synthetic construct' ? 32630 ? 2 1 sample 1 11 'synthetic construct' ? 32630 ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 IRI non-polymer . 'IRIDIUM HEXAMMINE ION' ? 'H18 Ir N6 3' 294.400 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 1 1 C C A . n A 1 2 G 2 2 2 G G A . n A 1 3 U 3 3 3 U U A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 U 7 7 7 U U A . n A 1 8 A 8 8 8 A A A . n A 1 9 G 9 9 9 G G A . n A 1 10 G 10 10 10 G G A . n A 1 11 G 11 11 11 G G A . n A 1 12 C 12 12 12 C C A . n A 1 13 C 13 13 13 C C A . n A 1 14 A 14 14 14 A A A . n A 1 15 C 15 15 15 C C A . n A 1 16 G 16 16 16 G G A . n A 1 17 U 17 17 17 U U A . n A 1 18 U 18 18 18 U U A . n A 1 19 A 19 19 19 A A A . n A 1 20 A 20 20 20 A A A . n A 1 21 A 21 21 21 A A A . n A 1 22 U 22 22 22 U U A . n A 1 23 A 23 23 23 A A A . n A 1 24 G 24 24 24 G G A . n A 1 25 U 25 25 25 U U A . n A 1 26 U 26 26 26 U U A . n A 1 27 G 27 27 27 G G A . n A 1 28 C 28 28 28 C C A . n A 1 29 U 29 29 29 U U A . n A 1 30 U 30 30 30 U U A . n A 1 31 A 31 31 31 A A A . n A 1 32 A 32 32 32 A A A . n A 1 33 G 33 33 33 G G A . n A 1 34 C 34 34 34 C C A . n A 1 35 C 35 35 35 C C A . n A 1 36 C 36 36 36 C C A . n A 1 37 U 37 37 37 U U A . n A 1 38 A 38 38 38 A A A . n A 1 39 A 39 39 39 A A A . n A 1 40 G 40 40 40 G G A . n A 1 41 C 41 41 41 C C A . n A 1 42 G 42 42 42 G G A . n A 1 43 U 43 43 43 U U A . n A 1 44 U 44 44 44 U U A . n A 1 45 G 45 45 45 G G A . n A 1 46 A 46 46 46 A A A . n A 1 47 U 47 47 47 U U A . n B 2 1 A 1 48 48 A A B . n B 2 2 U 2 49 49 U U B . n B 2 3 C 3 50 50 C C B . n B 2 4 A 4 51 51 A A B . n B 2 5 G 5 52 52 G G B . n B 2 6 DG 6 53 53 DG DG B . n B 2 7 U 7 54 54 U U B . n B 2 8 G 8 55 55 G G B . n B 2 9 C 9 56 56 C C B . n B 2 10 A 10 57 57 A A B . n B 2 11 A 11 58 58 A A B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 IRI 1 101 2 IRI IRI A . D 4 MG 1 102 1 MG MG A . E 4 MG 1 103 2 MG MG A . F 4 MG 1 104 4 MG MG A . G 4 MG 1 105 5 MG MG A . H 3 IRI 1 101 1 IRI IRI B . I 4 MG 1 102 3 MG MG B . J 5 HOH 1 201 4 HOH HOH A . J 5 HOH 2 202 2 HOH HOH A . J 5 HOH 3 203 9 HOH HOH A . J 5 HOH 4 204 3 HOH HOH A . J 5 HOH 5 205 5 HOH HOH A . J 5 HOH 6 206 6 HOH HOH A . J 5 HOH 7 207 14 HOH HOH A . J 5 HOH 8 208 8 HOH HOH A . J 5 HOH 9 209 11 HOH HOH A . J 5 HOH 10 210 10 HOH HOH A . J 5 HOH 11 211 1 HOH HOH A . J 5 HOH 12 212 13 HOH HOH A . J 5 HOH 13 213 15 HOH HOH A . K 5 HOH 1 201 7 HOH HOH B . K 5 HOH 2 202 12 HOH HOH B . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? AutoSol ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 5K7D _cell.details ? _cell.formula_units_Z ? _cell.length_a 56.573 _cell.length_a_esd ? _cell.length_b 56.573 _cell.length_b_esd ? _cell.length_c 88.297 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 6 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K7D _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5K7D _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 43.69 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.1 M Na-cacodylate, pH 6.5, Mg(OAc)2 0.2 M and 32% MPD and supplemented with 5 mM Ir(NH3)63+Cl3' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 6M-F' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-03-15 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.1052 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 24-ID-C' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.1052 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 24-ID-C _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5K7D _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.68 _reflns.d_resolution_low 88.3 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 8819 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.8 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.2 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 14.9 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all 0.038 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.68 _reflns_shell.d_res_low 2.81 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.2 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all ? _reflns_shell.percent_possible_obs 100 _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 6.4 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all 0.618 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 5K7D _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.68 _refine.ls_d_res_low 49 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 8819 _refine.ls_number_reflns_R_free 451 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.8 _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free 0.24 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.19 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1237 _refine_hist.pdbx_number_atoms_ligand 19 _refine_hist.number_atoms_solvent 15 _refine_hist.number_atoms_total 1271 _refine_hist.d_res_high 2.68 _refine_hist.d_res_low 49 # _struct.entry_id 5K7D _struct.title 'The structure of native pistol ribozyme, bound to Iridium' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 5K7D _struct_keywords.text 'ribozyme, RNA structure, pistol, RNA-DNA complex' _struct_keywords.pdbx_keywords RNA/DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 4 ? G N N 4 ? H N N 3 ? I N N 4 ? J N N 5 ? K N N 5 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 5K7D 5K7D ? 1 ? 1 2 PDB 5K7D 5K7D ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 5K7D A 1 ? 47 ? 5K7D 1 ? 47 ? 1 47 2 2 5K7D B 1 ? 11 ? 5K7D 48 ? 58 ? 48 58 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2530 ? 1 MORE -46 ? 1 'SSA (A^2)' 9350 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A C 41 OP2 ? ? ? 1_555 D MG . MG ? ? A C 41 A MG 102 1_555 ? ? ? ? ? ? ? 2.295 ? ? metalc2 metalc ? ? A G 42 OP2 ? ? ? 1_555 D MG . MG ? ? A G 42 A MG 102 1_555 ? ? ? ? ? ? ? 1.900 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 102 A HOH 201 1_555 ? ? ? ? ? ? ? 2.053 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 102 A HOH 202 1_555 ? ? ? ? ? ? ? 2.141 ? ? metalc5 metalc ? ? D MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 102 A HOH 204 1_555 ? ? ? ? ? ? ? 2.030 ? ? metalc6 metalc ? ? D MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 102 A HOH 205 1_555 ? ? ? ? ? ? ? 2.233 ? ? metalc7 metalc ? ? E MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 103 A HOH 203 1_555 ? ? ? ? ? ? ? 2.069 ? ? metalc8 metalc ? ? E MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 103 A HOH 208 1_555 ? ? ? ? ? ? ? 2.016 ? ? metalc9 metalc ? ? E MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 103 A HOH 211 1_555 ? ? ? ? ? ? ? 2.031 ? ? metalc10 metalc ? ? F MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 104 A HOH 209 1_555 ? ? ? ? ? ? ? 2.034 ? ? metalc11 metalc ? ? F MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 104 A HOH 212 1_555 ? ? ? ? ? ? ? 2.053 ? ? metalc12 metalc ? ? G MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 105 A HOH 207 1_555 ? ? ? ? ? ? ? 2.044 ? ? metalc13 metalc ? ? G MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 105 A HOH 210 1_555 ? ? ? ? ? ? ? 2.089 ? ? metalc14 metalc ? ? G MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 105 A HOH 213 1_555 ? ? ? ? ? ? ? 2.062 ? ? metalc15 metalc ? ? I MG . MG ? ? ? 1_555 K HOH . O ? ? B MG 102 B HOH 201 1_555 ? ? ? ? ? ? ? 2.121 ? ? metalc16 metalc ? ? I MG . MG ? ? ? 1_555 K HOH . O ? ? B MG 102 B HOH 202 1_555 ? ? ? ? ? ? ? 2.119 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 16 N2 ? ? A C 1 A G 16 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog2 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 16 N1 ? ? A C 1 A G 16 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog3 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 2 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 2 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 2 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 N2 ? ? ? 1_555 A U 18 O4 ? ? A G 2 A U 18 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 14 N1 ? ? A U 3 A A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 14 N6 ? ? A U 3 A A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 3 O2 ? ? ? 1_555 A A 19 N6 ? ? A U 3 A A 19 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 4 N2 ? ? ? 1_555 A A 21 N1 ? ? A G 4 A A 21 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog14 hydrog ? ? A G 4 N3 ? ? ? 1_555 A A 21 N6 ? ? A G 4 A A 21 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog15 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 12 N3 ? ? A G 5 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 12 O2 ? ? A G 5 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 12 N4 ? ? A G 5 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 5 N2 ? ? ? 1_555 A G 24 N3 ? ? A G 5 A G 24 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog19 hydrog ? ? A G 5 N3 ? ? ? 1_555 A G 24 N2 ? ? A G 5 A G 24 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog20 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 39 N1 ? ? A U 6 A A 39 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog21 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 38 N1 ? ? A U 7 A A 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 38 N6 ? ? A U 7 A A 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 37 N3 ? ? A A 8 A U 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 37 O4 ? ? A A 8 A U 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 36 N3 ? ? A G 9 A C 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 36 O2 ? ? A G 9 A C 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 36 N4 ? ? A G 9 A C 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 35 N3 ? ? A G 10 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 35 O2 ? ? A G 10 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 35 N4 ? ? A G 10 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 34 N3 ? ? A G 11 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 34 O2 ? ? A G 11 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 34 N4 ? ? A G 11 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A A 14 N3 ? ? ? 1_555 A A 20 N6 ? ? A A 14 A A 20 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog35 hydrog ? ? A C 15 O2 ? ? ? 1_555 A A 19 N6 ? ? A C 15 A A 19 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog36 hydrog ? ? A U 25 N3 ? ? ? 1_555 B A 11 N1 ? ? A U 25 B A 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A U 25 O4 ? ? ? 1_555 B A 11 N6 ? ? A U 25 B A 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 26 N3 ? ? ? 1_555 B A 10 N1 ? ? A U 26 B A 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A U 26 O4 ? ? ? 1_555 B A 10 N6 ? ? A U 26 B A 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 27 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 27 B C 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 27 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 27 B C 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 27 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 27 B C 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 28 N3 ? ? ? 1_555 B G 8 N2 ? ? A C 28 B G 55 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog44 hydrog ? ? A C 28 O2 ? ? ? 1_555 B G 8 N1 ? ? A C 28 B G 55 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog45 hydrog ? ? A U 29 N3 ? ? ? 1_555 B U 7 O4 ? ? A U 29 B U 54 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog46 hydrog ? ? A U 29 O2 ? ? ? 1_555 B U 7 N3 ? ? A U 29 B U 54 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog47 hydrog ? ? A G 33 O6 ? ? ? 1_555 A G 40 N2 ? ? A G 33 A G 40 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog48 hydrog ? ? A G 33 N1 ? ? ? 1_555 A C 41 N3 ? ? A G 33 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 33 N2 ? ? ? 1_555 A C 41 O2 ? ? A G 33 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A G 33 O6 ? ? ? 1_555 A C 41 N4 ? ? A G 33 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A A 39 N1 ? ? ? 1_555 A C 41 N4 ? ? A A 39 A C 41 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog52 hydrog ? ? A G 40 N2 ? ? ? 1_555 A G 42 O6 ? ? A G 40 A G 42 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog53 hydrog ? ? A G 42 O6 ? ? ? 1_555 B DG 6 N2 ? ? A G 42 B DG 53 1_555 ? ? ? ? ? ? 'G-DG MISPAIR' ? ? ? hydrog54 hydrog ? ? A U 43 O4 ? ? ? 1_555 B G 5 N2 ? ? A U 43 B G 52 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog55 hydrog ? ? A U 43 O4 ? ? ? 1_555 B DG 6 N2 ? ? A U 43 B DG 53 1_555 ? ? ? ? ? ? 'U-DG MISPAIR' ? ? ? hydrog56 hydrog ? ? A U 44 N3 ? ? ? 1_555 B A 4 N1 ? ? A U 44 B A 51 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog57 hydrog ? ? A G 45 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 45 B C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A G 45 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 45 B C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A G 45 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 45 B C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A A 46 N1 ? ? ? 1_555 B U 2 N3 ? ? A A 46 B U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A A 46 N6 ? ? ? 1_555 B U 2 O4 ? ? A A 46 B U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP2 ? A C 41 ? A C 41 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 OP2 ? A G 42 ? A G 42 ? 1_555 69.9 ? 2 OP2 ? A C 41 ? A C 41 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 201 ? 1_555 53.6 ? 3 OP2 ? A G 42 ? A G 42 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 201 ? 1_555 120.2 ? 4 OP2 ? A C 41 ? A C 41 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 202 ? 1_555 70.3 ? 5 OP2 ? A G 42 ? A G 42 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 202 ? 1_555 72.2 ? 6 O ? J HOH . ? A HOH 201 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 202 ? 1_555 71.8 ? 7 OP2 ? A C 41 ? A C 41 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 204 ? 1_555 129.3 ? 8 OP2 ? A G 42 ? A G 42 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 204 ? 1_555 85.4 ? 9 O ? J HOH . ? A HOH 201 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 204 ? 1_555 114.1 ? 10 O ? J HOH . ? A HOH 202 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 204 ? 1_555 60.0 ? 11 OP2 ? A C 41 ? A C 41 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 205 ? 1_555 78.7 ? 12 OP2 ? A G 42 ? A G 42 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 205 ? 1_555 107.8 ? 13 O ? J HOH . ? A HOH 201 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 205 ? 1_555 81.0 ? 14 O ? J HOH . ? A HOH 202 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 205 ? 1_555 147.0 ? 15 O ? J HOH . ? A HOH 204 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? J HOH . ? A HOH 205 ? 1_555 152.1 ? 16 O ? J HOH . ? A HOH 203 ? 1_555 MG ? E MG . ? A MG 103 ? 1_555 O ? J HOH . ? A HOH 208 ? 1_555 171.4 ? 17 O ? J HOH . ? A HOH 203 ? 1_555 MG ? E MG . ? A MG 103 ? 1_555 O ? J HOH . ? A HOH 211 ? 1_555 115.1 ? 18 O ? J HOH . ? A HOH 208 ? 1_555 MG ? E MG . ? A MG 103 ? 1_555 O ? J HOH . ? A HOH 211 ? 1_555 62.6 ? 19 O ? J HOH . ? A HOH 209 ? 1_555 MG ? F MG . ? A MG 104 ? 1_555 O ? J HOH . ? A HOH 212 ? 1_555 67.8 ? 20 O ? J HOH . ? A HOH 207 ? 1_555 MG ? G MG . ? A MG 105 ? 1_555 O ? J HOH . ? A HOH 210 ? 1_555 87.3 ? 21 O ? J HOH . ? A HOH 207 ? 1_555 MG ? G MG . ? A MG 105 ? 1_555 O ? J HOH . ? A HOH 213 ? 1_555 83.7 ? 22 O ? J HOH . ? A HOH 210 ? 1_555 MG ? G MG . ? A MG 105 ? 1_555 O ? J HOH . ? A HOH 213 ? 1_555 64.7 ? 23 O ? K HOH . ? B HOH 201 ? 1_555 MG ? I MG . ? B MG 102 ? 1_555 O ? K HOH . ? B HOH 202 ? 1_555 103.1 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A IRI 101 ? 7 'binding site for residue IRI A 101' AC2 Software A MG 102 ? 6 'binding site for residue MG A 102' AC3 Software A MG 103 ? 4 'binding site for residue MG A 103' AC4 Software A MG 104 ? 4 'binding site for residue MG A 104' AC5 Software A MG 105 ? 4 'binding site for residue MG A 105' AC6 Software B IRI 101 ? 3 'binding site for residue IRI B 101' AC7 Software B MG 102 ? 4 'binding site for residue MG B 102' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 7 G A 5 ? G A 5 . ? 1_555 ? 2 AC1 7 U A 7 ? U A 7 . ? 1_555 ? 3 AC1 7 A A 8 ? A A 8 . ? 1_555 ? 4 AC1 7 G A 9 ? G A 9 . ? 1_555 ? 5 AC1 7 G A 10 ? G A 10 . ? 1_555 ? 6 AC1 7 G A 11 ? G A 11 . ? 1_555 ? 7 AC1 7 C A 34 ? C A 34 . ? 1_555 ? 8 AC2 6 C A 41 ? C A 41 . ? 1_555 ? 9 AC2 6 G A 42 ? G A 42 . ? 1_555 ? 10 AC2 6 HOH J . ? HOH A 201 . ? 1_555 ? 11 AC2 6 HOH J . ? HOH A 202 . ? 1_555 ? 12 AC2 6 HOH J . ? HOH A 204 . ? 1_555 ? 13 AC2 6 HOH J . ? HOH A 205 . ? 1_555 ? 14 AC3 4 G A 33 ? G A 33 . ? 1_555 ? 15 AC3 4 HOH J . ? HOH A 203 . ? 1_555 ? 16 AC3 4 HOH J . ? HOH A 208 . ? 1_555 ? 17 AC3 4 HOH J . ? HOH A 211 . ? 1_555 ? 18 AC4 4 U A 37 ? U A 37 . ? 1_555 ? 19 AC4 4 A A 38 ? A A 38 . ? 1_555 ? 20 AC4 4 HOH J . ? HOH A 209 . ? 1_555 ? 21 AC4 4 HOH J . ? HOH A 212 . ? 1_555 ? 22 AC5 4 A A 23 ? A A 23 . ? 1_555 ? 23 AC5 4 HOH J . ? HOH A 207 . ? 1_555 ? 24 AC5 4 HOH J . ? HOH A 210 . ? 1_555 ? 25 AC5 4 HOH J . ? HOH A 213 . ? 1_555 ? 26 AC6 3 G B 5 ? G B 52 . ? 1_555 ? 27 AC6 3 DG B 6 ? DG B 53 . ? 1_555 ? 28 AC6 3 MG I . ? MG B 102 . ? 1_555 ? 29 AC7 4 DG B 6 ? DG B 53 . ? 1_555 ? 30 AC7 4 IRI H . ? IRI B 101 . ? 1_555 ? 31 AC7 4 HOH K . ? HOH B 201 . ? 1_555 ? 32 AC7 4 HOH K . ? HOH B 202 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 OP2 A C 41 ? ? O A HOH 201 ? ? 1.97 2 1 O2 A C 1 ? ? N2 A G 16 ? ? 2.03 3 1 O A HOH 202 ? ? O A HOH 204 ? ? 2.09 4 1 O A HOH 208 ? ? O A HOH 211 ? ? 2.10 5 1 O2 A C 28 ? ? N2 B G 55 ? ? 2.16 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DG _pdbx_validate_rmsd_bond.auth_seq_id_1 53 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DG _pdbx_validate_rmsd_bond.auth_seq_id_2 53 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.371 _pdbx_validate_rmsd_bond.bond_target_value 1.419 _pdbx_validate_rmsd_bond.bond_deviation -0.048 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag N # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 A _pdbx_validate_rmsd_angle.auth_seq_id_1 19 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 A _pdbx_validate_rmsd_angle.auth_seq_id_2 19 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N9 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 A _pdbx_validate_rmsd_angle.auth_seq_id_3 19 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 113.71 _pdbx_validate_rmsd_angle.angle_target_value 108.50 _pdbx_validate_rmsd_angle.angle_deviation 5.21 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.70 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 DG OP3 O N N 73 DG P P N N 74 DG OP1 O N N 75 DG OP2 O N N 76 DG "O5'" O N N 77 DG "C5'" C N N 78 DG "C4'" C N R 79 DG "O4'" O N N 80 DG "C3'" C N S 81 DG "O3'" O N N 82 DG "C2'" C N N 83 DG "C1'" C N R 84 DG N9 N Y N 85 DG C8 C Y N 86 DG N7 N Y N 87 DG C5 C Y N 88 DG C6 C N N 89 DG O6 O N N 90 DG N1 N N N 91 DG C2 C N N 92 DG N2 N N N 93 DG N3 N N N 94 DG C4 C Y N 95 DG HOP3 H N N 96 DG HOP2 H N N 97 DG "H5'" H N N 98 DG "H5''" H N N 99 DG "H4'" H N N 100 DG "H3'" H N N 101 DG "HO3'" H N N 102 DG "H2'" H N N 103 DG "H2''" H N N 104 DG "H1'" H N N 105 DG H8 H N N 106 DG H1 H N N 107 DG H21 H N N 108 DG H22 H N N 109 G OP3 O N N 110 G P P N N 111 G OP1 O N N 112 G OP2 O N N 113 G "O5'" O N N 114 G "C5'" C N N 115 G "C4'" C N R 116 G "O4'" O N N 117 G "C3'" C N S 118 G "O3'" O N N 119 G "C2'" C N R 120 G "O2'" O N N 121 G "C1'" C N R 122 G N9 N Y N 123 G C8 C Y N 124 G N7 N Y N 125 G C5 C Y N 126 G C6 C N N 127 G O6 O N N 128 G N1 N N N 129 G C2 C N N 130 G N2 N N N 131 G N3 N N N 132 G C4 C Y N 133 G HOP3 H N N 134 G HOP2 H N N 135 G "H5'" H N N 136 G "H5''" H N N 137 G "H4'" H N N 138 G "H3'" H N N 139 G "HO3'" H N N 140 G "H2'" H N N 141 G "HO2'" H N N 142 G "H1'" H N N 143 G H8 H N N 144 G H1 H N N 145 G H21 H N N 146 G H22 H N N 147 HOH O O N N 148 HOH H1 H N N 149 HOH H2 H N N 150 IRI IR IR N N 151 IRI N1 N N N 152 IRI N2 N N N 153 IRI N3 N N N 154 IRI N4 N N N 155 IRI N5 N N N 156 IRI N6 N N N 157 IRI HN11 H N N 158 IRI HN12 H N N 159 IRI HN13 H N N 160 IRI HN21 H N N 161 IRI HN22 H N N 162 IRI HN23 H N N 163 IRI HN31 H N N 164 IRI HN32 H N N 165 IRI HN33 H N N 166 IRI HN41 H N N 167 IRI HN42 H N N 168 IRI HN43 H N N 169 IRI HN51 H N N 170 IRI HN52 H N N 171 IRI HN53 H N N 172 IRI HN61 H N N 173 IRI HN62 H N N 174 IRI HN63 H N N 175 MG MG MG N N 176 U OP3 O N N 177 U P P N N 178 U OP1 O N N 179 U OP2 O N N 180 U "O5'" O N N 181 U "C5'" C N N 182 U "C4'" C N R 183 U "O4'" O N N 184 U "C3'" C N S 185 U "O3'" O N N 186 U "C2'" C N R 187 U "O2'" O N N 188 U "C1'" C N R 189 U N1 N N N 190 U C2 C N N 191 U O2 O N N 192 U N3 N N N 193 U C4 C N N 194 U O4 O N N 195 U C5 C N N 196 U C6 C N N 197 U HOP3 H N N 198 U HOP2 H N N 199 U "H5'" H N N 200 U "H5''" H N N 201 U "H4'" H N N 202 U "H3'" H N N 203 U "HO3'" H N N 204 U "H2'" H N N 205 U "HO2'" H N N 206 U "H1'" H N N 207 U H3 H N N 208 U H5 H N N 209 U H6 H N N 210 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 DG OP3 P sing N N 76 DG OP3 HOP3 sing N N 77 DG P OP1 doub N N 78 DG P OP2 sing N N 79 DG P "O5'" sing N N 80 DG OP2 HOP2 sing N N 81 DG "O5'" "C5'" sing N N 82 DG "C5'" "C4'" sing N N 83 DG "C5'" "H5'" sing N N 84 DG "C5'" "H5''" sing N N 85 DG "C4'" "O4'" sing N N 86 DG "C4'" "C3'" sing N N 87 DG "C4'" "H4'" sing N N 88 DG "O4'" "C1'" sing N N 89 DG "C3'" "O3'" sing N N 90 DG "C3'" "C2'" sing N N 91 DG "C3'" "H3'" sing N N 92 DG "O3'" "HO3'" sing N N 93 DG "C2'" "C1'" sing N N 94 DG "C2'" "H2'" sing N N 95 DG "C2'" "H2''" sing N N 96 DG "C1'" N9 sing N N 97 DG "C1'" "H1'" sing N N 98 DG N9 C8 sing Y N 99 DG N9 C4 sing Y N 100 DG C8 N7 doub Y N 101 DG C8 H8 sing N N 102 DG N7 C5 sing Y N 103 DG C5 C6 sing N N 104 DG C5 C4 doub Y N 105 DG C6 O6 doub N N 106 DG C6 N1 sing N N 107 DG N1 C2 sing N N 108 DG N1 H1 sing N N 109 DG C2 N2 sing N N 110 DG C2 N3 doub N N 111 DG N2 H21 sing N N 112 DG N2 H22 sing N N 113 DG N3 C4 sing N N 114 G OP3 P sing N N 115 G OP3 HOP3 sing N N 116 G P OP1 doub N N 117 G P OP2 sing N N 118 G P "O5'" sing N N 119 G OP2 HOP2 sing N N 120 G "O5'" "C5'" sing N N 121 G "C5'" "C4'" sing N N 122 G "C5'" "H5'" sing N N 123 G "C5'" "H5''" sing N N 124 G "C4'" "O4'" sing N N 125 G "C4'" "C3'" sing N N 126 G "C4'" "H4'" sing N N 127 G "O4'" "C1'" sing N N 128 G "C3'" "O3'" sing N N 129 G "C3'" "C2'" sing N N 130 G "C3'" "H3'" sing N N 131 G "O3'" "HO3'" sing N N 132 G "C2'" "O2'" sing N N 133 G "C2'" "C1'" sing N N 134 G "C2'" "H2'" sing N N 135 G "O2'" "HO2'" sing N N 136 G "C1'" N9 sing N N 137 G "C1'" "H1'" sing N N 138 G N9 C8 sing Y N 139 G N9 C4 sing Y N 140 G C8 N7 doub Y N 141 G C8 H8 sing N N 142 G N7 C5 sing Y N 143 G C5 C6 sing N N 144 G C5 C4 doub Y N 145 G C6 O6 doub N N 146 G C6 N1 sing N N 147 G N1 C2 sing N N 148 G N1 H1 sing N N 149 G C2 N2 sing N N 150 G C2 N3 doub N N 151 G N2 H21 sing N N 152 G N2 H22 sing N N 153 G N3 C4 sing N N 154 HOH O H1 sing N N 155 HOH O H2 sing N N 156 IRI IR N1 sing N N 157 IRI IR N2 sing N N 158 IRI IR N3 sing N N 159 IRI IR N4 sing N N 160 IRI IR N5 sing N N 161 IRI IR N6 sing N N 162 IRI N1 HN11 sing N N 163 IRI N1 HN12 sing N N 164 IRI N1 HN13 sing N N 165 IRI N2 HN21 sing N N 166 IRI N2 HN22 sing N N 167 IRI N2 HN23 sing N N 168 IRI N3 HN31 sing N N 169 IRI N3 HN32 sing N N 170 IRI N3 HN33 sing N N 171 IRI N4 HN41 sing N N 172 IRI N4 HN42 sing N N 173 IRI N4 HN43 sing N N 174 IRI N5 HN51 sing N N 175 IRI N5 HN52 sing N N 176 IRI N5 HN53 sing N N 177 IRI N6 HN61 sing N N 178 IRI N6 HN62 sing N N 179 IRI N6 HN63 sing N N 180 U OP3 P sing N N 181 U OP3 HOP3 sing N N 182 U P OP1 doub N N 183 U P OP2 sing N N 184 U P "O5'" sing N N 185 U OP2 HOP2 sing N N 186 U "O5'" "C5'" sing N N 187 U "C5'" "C4'" sing N N 188 U "C5'" "H5'" sing N N 189 U "C5'" "H5''" sing N N 190 U "C4'" "O4'" sing N N 191 U "C4'" "C3'" sing N N 192 U "C4'" "H4'" sing N N 193 U "O4'" "C1'" sing N N 194 U "C3'" "O3'" sing N N 195 U "C3'" "C2'" sing N N 196 U "C3'" "H3'" sing N N 197 U "O3'" "HO3'" sing N N 198 U "C2'" "O2'" sing N N 199 U "C2'" "C1'" sing N N 200 U "C2'" "H2'" sing N N 201 U "O2'" "HO2'" sing N N 202 U "C1'" N1 sing N N 203 U "C1'" "H1'" sing N N 204 U N1 C2 sing N N 205 U N1 C6 sing N N 206 U C2 O2 doub N N 207 U C2 N3 sing N N 208 U N3 C4 sing N N 209 U N3 H3 sing N N 210 U C4 O4 doub N N 211 U C4 C5 sing N N 212 U C5 C6 doub N N 213 U C5 H5 sing N N 214 U C6 H6 sing N N 215 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5K7D 'double helix' 5K7D 'a-form double helix' 5K7D 'bulge loop' 5K7D 'triple helix' 5K7D 'quadruple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 1 1_555 A G 16 1_555 0.122 -0.777 0.145 -5.165 -3.265 2.560 1 A_C1:G16_A A 1 ? A 16 ? 22 1 1 A G 2 1_555 A C 15 1_555 -0.275 -0.193 -0.139 -5.969 -14.300 0.931 2 A_G2:C15_A A 2 ? A 15 ? 19 1 1 A U 3 1_555 A A 14 1_555 0.098 -0.112 0.024 -3.465 -11.791 2.722 3 A_U3:A14_A A 3 ? A 14 ? 20 1 1 A G 4 1_555 A C 13 1_555 -0.301 -0.312 0.403 3.833 -6.143 -0.145 4 A_G4:C13_A A 4 ? A 13 ? 19 1 1 A G 5 1_555 A C 12 1_555 -0.084 -0.182 0.172 9.600 -1.546 -1.573 5 A_G5:C12_A A 5 ? A 12 ? 19 1 1 A C 34 1_555 A G 11 1_555 0.191 -0.191 -0.086 10.454 -12.867 1.378 6 A_C34:G11_A A 34 ? A 11 ? 19 1 1 A C 35 1_555 A G 10 1_555 0.086 -0.189 0.073 1.290 -11.487 0.452 7 A_C35:G10_A A 35 ? A 10 ? 19 1 1 A C 36 1_555 A G 9 1_555 0.100 -0.143 0.352 -4.000 -8.239 0.384 8 A_C36:G9_A A 36 ? A 9 ? 19 1 1 A U 37 1_555 A A 8 1_555 -0.112 -0.095 0.194 -2.636 -1.237 3.010 9 A_U37:A8_A A 37 ? A 8 ? 20 1 1 A A 38 1_555 A U 7 1_555 0.241 -0.008 0.332 0.029 -5.405 -1.437 10 A_A38:U7_A A 38 ? A 7 ? 20 1 1 A A 39 1_555 A U 6 1_555 1.038 0.168 0.795 -11.949 -9.478 2.937 11 A_A39:U6_A A 39 ? A 6 ? ? ? 1 A C 41 1_555 A G 33 1_555 0.188 -0.213 0.609 -1.204 -2.946 0.500 12 A_C41:G33_A A 41 ? A 33 ? 19 1 1 A G 42 1_555 B DG 6 1_555 -6.840 -2.043 -1.036 9.736 1.314 -3.344 13 A_G42:DG53_B A 42 ? B 53 ? ? ? 1 A U 43 1_555 B G 5 1_555 -4.146 0.583 -1.747 25.566 -16.622 11.139 14 A_U43:G52_B A 43 ? B 52 ? ? ? 1 A U 44 1_555 B A 4 1_555 0.733 0.453 0.046 1.590 -5.269 8.077 15 A_U44:A51_B A 44 ? B 51 ? ? ? 1 A G 45 1_555 B C 3 1_555 0.450 -0.106 -0.013 -0.855 -9.262 0.320 16 A_G45:C50_B A 45 ? B 50 ? 19 1 1 A A 46 1_555 B U 2 1_555 0.368 0.155 0.195 5.465 -4.037 -1.297 17 A_A46:U49_B A 46 ? B 49 ? 20 1 1 A U 25 1_555 B A 11 1_555 -0.274 0.091 0.210 -9.642 1.384 -4.398 18 A_U25:A58_B A 25 ? B 58 ? 20 1 1 A U 26 1_555 B A 10 1_555 -0.325 -0.065 0.111 -6.167 4.295 10.834 19 A_U26:A57_B A 26 ? B 57 ? 20 1 1 A G 27 1_555 B C 9 1_555 0.552 -0.074 -0.053 5.818 4.222 6.020 20 A_G27:C56_B A 27 ? B 56 ? 19 1 1 A C 28 1_555 B G 8 1_555 0.538 -0.030 -0.363 11.299 -4.044 15.723 21 A_C28:G55_B A 28 ? B 55 ? 22 1 1 A U 29 1_555 B U 7 1_555 2.477 -2.341 0.397 11.284 -12.598 14.750 22 A_U29:U54_B A 29 ? B 54 ? 16 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 1 1_555 A G 16 1_555 A G 2 1_555 A C 15 1_555 -0.106 -1.711 3.145 1.372 7.759 28.334 -4.860 0.472 2.587 15.475 -2.737 29.388 1 AA_C1G2:C15G16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A G 2 1_555 A C 15 1_555 A U 3 1_555 A A 14 1_555 0.229 -0.708 3.246 -0.913 4.410 33.489 -1.916 -0.538 3.123 7.610 1.575 33.781 2 AA_G2U3:A14C15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A U 3 1_555 A A 14 1_555 A G 4 1_555 A C 13 1_555 -0.250 -1.399 2.850 -2.820 7.758 30.952 -3.692 0.034 2.449 14.222 5.169 32.008 3 AA_U3G4:C13A14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A G 4 1_555 A C 13 1_555 A G 5 1_555 A C 12 1_555 -0.775 -1.981 3.214 1.307 7.878 28.497 -5.380 1.767 2.549 15.620 -2.591 29.572 4 AA_G4G5:C12C13_AA A 4 ? A 13 ? A 5 ? A 12 ? 1 A G 5 1_555 A C 12 1_555 A C 34 1_555 A G 11 1_555 -1.718 -0.763 3.160 -1.459 3.829 48.546 -1.207 1.975 3.142 4.648 1.771 48.708 5 AA_G5C34:G11C12_AA A 5 ? A 12 ? A 34 ? A 11 ? 1 A C 34 1_555 A G 11 1_555 A C 35 1_555 A G 10 1_555 -0.781 -1.980 3.251 -4.926 12.673 32.304 -5.021 0.628 2.418 21.621 8.404 34.978 6 AA_C34C35:G10G11_AA A 34 ? A 11 ? A 35 ? A 10 ? 1 A C 35 1_555 A G 10 1_555 A C 36 1_555 A G 9 1_555 -0.761 -1.751 3.244 -4.820 12.081 29.311 -5.160 0.587 2.443 22.527 8.989 32.010 7 AA_C35C36:G9G10_AA A 35 ? A 10 ? A 36 ? A 9 ? 1 A C 36 1_555 A G 9 1_555 A U 37 1_555 A A 8 1_555 -0.368 -1.221 3.166 -0.683 12.739 30.875 -4.033 0.538 2.490 22.748 1.220 33.347 8 AA_C36U37:A8G9_AA A 36 ? A 9 ? A 37 ? A 8 ? 1 A U 37 1_555 A A 8 1_555 A A 38 1_555 A U 7 1_555 0.597 -1.282 3.045 3.663 12.274 33.319 -3.656 -0.509 2.484 20.489 -6.114 35.631 9 AA_U37A38:U7A8_AA A 37 ? A 8 ? A 38 ? A 7 ? 1 A A 38 1_555 A U 7 1_555 A A 39 1_555 A U 6 1_555 1.994 -2.201 3.301 7.037 9.904 34.084 -4.920 -2.242 2.911 16.269 -11.560 36.124 10 AA_A38A39:U6U7_AA A 38 ? A 7 ? A 39 ? A 6 ? 1 A A 39 1_555 A U 6 1_555 A C 41 1_555 A G 33 1_555 -1.240 -3.189 2.633 6.374 3.003 57.088 -3.439 1.553 2.338 3.130 -6.642 57.484 11 AA_A39C41:G33U6_AA A 39 ? A 6 ? A 41 ? A 33 ? 1 A C 41 1_555 A G 33 1_555 A G 42 1_555 B DG 6 1_555 4.225 0.695 3.538 3.607 -3.150 41.848 1.333 -5.461 3.813 -4.392 -5.030 42.109 12 AA_C41G42:DG53G33_BA A 41 ? A 33 ? A 42 ? B 53 ? 1 A G 42 1_555 B DG 6 1_555 A U 43 1_555 B G 5 1_555 0.571 -0.332 3.060 3.657 4.619 35.892 -1.136 -0.438 3.037 7.433 -5.886 36.357 13 AA_G42U43:G52DG53_BB A 42 ? B 53 ? A 43 ? B 52 ? 1 A U 43 1_555 B G 5 1_555 A U 44 1_555 B A 4 1_555 0.347 -1.464 4.425 -14.258 15.503 45.345 -3.195 -1.751 3.527 18.951 17.430 49.763 14 AA_U43U44:A51G52_BB A 43 ? B 52 ? A 44 ? B 51 ? 1 A U 44 1_555 B A 4 1_555 A G 45 1_555 B C 3 1_555 -1.141 -1.443 3.140 1.276 9.812 29.937 -4.281 2.313 2.504 18.374 -2.390 31.494 15 AA_U44G45:C50A51_BB A 44 ? B 51 ? A 45 ? B 50 ? 1 A G 45 1_555 B C 3 1_555 A A 46 1_555 B U 2 1_555 0.062 -1.776 2.963 -2.605 5.132 25.538 -5.110 -0.739 2.544 11.425 5.800 26.168 16 AA_G45A46:U49C50_BB A 45 ? B 50 ? A 46 ? B 49 ? 1 A U 25 1_555 B A 11 1_555 A U 26 1_555 B A 10 1_555 -0.036 -2.287 3.117 -2.226 1.503 24.634 -5.755 -0.544 2.966 3.509 5.197 24.778 17 AA_U25U26:A57A58_BB A 25 ? B 58 ? A 26 ? B 57 ? 1 A U 26 1_555 B A 10 1_555 A G 27 1_555 B C 9 1_555 -0.542 -1.145 2.908 -1.745 10.513 31.123 -3.536 0.707 2.429 18.912 3.138 32.854 18 AA_U26G27:C56A57_BB A 26 ? B 57 ? A 27 ? B 56 ? 1 A G 27 1_555 B C 9 1_555 A C 28 1_555 B G 8 1_555 0.715 -1.267 3.105 1.582 8.280 27.276 -4.270 -1.126 2.650 17.049 -3.257 28.525 19 AA_G27C28:G55C56_BB A 27 ? B 56 ? A 28 ? B 55 ? 1 A C 28 1_555 B G 8 1_555 A U 29 1_555 B U 7 1_555 0.521 -1.199 3.183 -3.098 3.851 37.910 -2.291 -1.165 3.001 5.897 4.744 38.219 20 AA_C28U29:U54G55_BB A 28 ? B 55 ? A 29 ? B 54 ? # _atom_sites.entry_id 5K7D _atom_sites.fract_transf_matrix[1][1] 0.017676 _atom_sites.fract_transf_matrix[1][2] 0.010205 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.020411 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.011325 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C IR MG N O P # loop_